Conservative NNs for FDR control

--- Resubmitted on 2026-03-30 15:28:10 UTC ---
Changes detected:
  Row count: 93813 → 92921
  Added columns: ['epsilon_precision_mean', 'epsilon_precision_median', 'log2_empirical_mean', 'log2_empirical_median']
Parameter corrections applied:
  ident_fdr_protein: 'None' → 'nan'
  ident_fdr_peptide: 'None' → 'nan'
--- PERSISTED_CORRECTIONS ---
CORRECTION:ident_fdr_protein=nan
CORRECTION:ident_fdr_peptide=nan
--- END_PERSISTED_CORRECTIONS ---